Cell-based clustering using pixel clusters: Gaussian blur sigma=2, k=20, arcsinh

Heatmaps of pixel clusters x markers

Compare pixel clusering with cell clustering

Cell-based FlowSOM clustering using all pixel clusters

No transformation

Normalize by total (covert from count to frequency), arcsinh transform, 99.99% normalization

Drop pixel clusters that do not have at least one marker ranked in top 5, normalize by total, arcsinh, 99.99% normalization

## [1] "Number of dropped clusters: 41"

## [1] "Dropped clusters: 1,2,3,4,5,6,7,8,9,10,11,12,13,15,16,17,18,23,24,25,26,27,28,29,31,35,42,49,50,51,53,56,57,58,60,63,64,73,76,82,87"

Cell-based FlowSOM clustering using pixel hierarchical clusters

No transformation

Normalize by total (covert from count to frequency), arcsinh transform, 99.99% normalization

Drop pixel clusters that do not have at least one marker ranked in top 2, normalize by total, arcsinh, 99.99% normalization

## [1] "Number of dropped clusters: 2"

## [1] "Dropped clusters: 1,3"